Immunoinformatic Analysis of SARS-CoV-2 Nucleocapsid Protein and Identification of COVID-19 Vaccine Targets

Front Immunol. 2020 Oct 28:11:587615. doi: 10.3389/fimmu.2020.587615. eCollection 2020.

Abstract

COVID-19 is a worldwide emergency; therefore, there is a critical need for foundational knowledge about B and T cell responses to SARS-CoV-2 essential for vaccine development. However, little information is available defining which determinants of SARS-CoV-2 other than the spike glycoprotein are recognized by the host immune system. In this study, we focus on the SARS-CoV-2 nucleocapsid protein as a suitable candidate target for vaccine formulations. Major B and T cell epitopes of the SARS-CoV-2 N protein are predicted and resulting sequences compared with the homolog immunological domains of other coronaviruses that infect human beings. The most dominant of B cell epitope is located between 176-206 amino acids in the SRGGSQASSRSSSRSRNSSRNSTPGSSRGTS sequence. Further, we identify sequences which are predicted to bind multiple common MHC I and MHC II alleles. Most notably there is a region of potential T cell cross-reactivity within the SARS-CoV-2 N protein position 102-110 amino acids that traverses multiple human alpha and betacoronaviruses. Vaccination strategies designed to target these conserved epitope regions could generate immune responses that are cross-reactive across human coronaviruses, with potential to protect or modulate disease. Finally, these predictions can facilitate effective vaccine design against this high priority virus.

Keywords: B cells; Coronavirus Disease 2019; T cells; epitopes; nucleocapsid; severe acute respiratory syndrome coronavirus 2; vaccine.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 / immunology
  • COVID-19 / prevention & control
  • COVID-19 / virology*
  • COVID-19 Vaccines / chemistry
  • COVID-19 Vaccines / genetics
  • COVID-19 Vaccines / immunology*
  • Computational Biology
  • Coronavirus Nucleocapsid Proteins / chemistry
  • Coronavirus Nucleocapsid Proteins / genetics
  • Coronavirus Nucleocapsid Proteins / immunology*
  • Epitope Mapping
  • Epitopes, B-Lymphocyte / chemistry
  • Epitopes, B-Lymphocyte / genetics
  • Epitopes, B-Lymphocyte / immunology
  • Epitopes, T-Lymphocyte / chemistry
  • Epitopes, T-Lymphocyte / genetics
  • Epitopes, T-Lymphocyte / immunology
  • Humans
  • Immunogenicity, Vaccine
  • SARS-CoV-2 / chemistry
  • SARS-CoV-2 / genetics
  • SARS-CoV-2 / immunology*

Substances

  • COVID-19 Vaccines
  • Coronavirus Nucleocapsid Proteins
  • Epitopes, B-Lymphocyte
  • Epitopes, T-Lymphocyte